In the 21st century, Starman, working as a caretaker, digs up a grave with the name "Kent". In the 31st century, the Legion continues to battle the villians while Bart Allen pounds Superboy-Prime. Brainiac 5 explains that the team of Legionnaires recently sent back in time used the lightning rod to "bottle up" Bart's essence before his death at the hands of the Rogues. Brainiac 5 says that Dream Girl foresaw Superboy-Prime destroying Earth in a massive Crisis but vanished before she could give more details.

Kid Flash knocks Superboy-Prime back into the battle when Superman and the original Lightning Lad, Saturn Girl and Cosmic Boy are pulled through a portal to the end of time where they face the Time Trapper who intends to kill the four of them. Kinetix attacks Superboy-Prime, who promptly kills her when her magic has no effect. Seeing the news reports of the battle and the casualties, the original Sun Boy grabs his flight ring while Mordru absorbs Kinetix's life force and magical knowledge.

The "Threeboot" Element Lad turns the ground into kryptonite. Superboy-Prime laughs before he suddenly convulses in pain and promptly kills the "Threeboot" Element Lad by throwing a kryptonite rock right through him. Cosmic King then turns the kryptonite inside Superboy-Prime into yellow sunlight. Mordru warns Superboy-Prime of a vision of the future showing the Legion of Super-Heroes victorious and Prime heads to the North Pole to cut them off.

At the Fortress of Solitude, the three Brainiacs meet Polar Boy, Dawnstar and Wildfire with a strand of Lex Luthor's hair. The original Brainiac 5 then puts the hair inside a Kryptonian chrysalis. However, Superboy-Prime attacks, knocking all three Brainiacs out. Polar Boy fights Prime and his ice hand is cut of when the original Sun Boy arrives to help. Wildfire uses his energies to fuel the chrysalis and resurrects Conner Kent, a.k.a Superboy, who then confronts Superboy-Prime.

Superboy and Superboy-Prime clash with the rest of the Legions joining in. At the end of time, Superman and the three founding Legionnaires attack the Time Trapper, tearing off his hood, only to realise that the Time Trapper is an aged Superboy-Prime, who claims the three heroic Legions will all lose.

In the 31st Century, Superboy-Prime fights off the three heroic Legions and Superboy. At the end of time, the three founding Legionnaires and Superman battle the elder Superboy-Prime aka Time Trapper, who reveals that he became an anomaly that couldn't be killed after being shunted into the Multiverse, plus that he can access other alternate realities and intends to destroy the Legions in each of those realities.

Superboy burns a scar on Superboy-Prime's chest, which also appears on the Time Trapper's chest. The original Saturn Girl and Brainiac 5 realize that time has become fluid, leading Brainiac 5 to deduce that the Time Trapper is a rogue sentient alternate timeline, and that his identity keeps changing with time.

Back in Metropolis, Mordru uses the magics he absorbed from Kinetix to weaken the 3 Legions and empower the Legion of Super-Villains. He then launches an injurious attack on Blok, forcing the White Witch to invoke one of Mordru's dark spells against Mordru that absorbs his life force into her own. Mysa, now calling herself the Black Witch, uses her new magics to defeat the Legion of Super-Villains. Bouncing Boy and Duo Damsel, now calling herself Duplicate Damsel, then appear, where Luornu reveals that she gained the ability make multiple copies of herself after her second body was killed in the 21st century.

At the end of time, the original founding Legionnaires use the Time Trapper's time portals to summon multiple Legions from across the Multiverse, who manage to knock the Trapper out. The founding Legionnaires and Superman then return to the 31st century with the Time Trapper. Superboy-Prime is repulsed by what he becomes, so he punches his future self, which erases both of them. The three Brainiacs reveal that the Time Trapper the Legion knew no longer exists as the future was reset when Superboy-Prime punched his elder self.

After the battle is over, Sodam Yat recharges power rings on Oa to rebuild the Green Lantern Corps. The Black Witch travels to Zerox and claims Mordru's throne. The "Reboot" Legion, under the guidance of Shikari, decide to travel the Multiverse looking for other survivors, with Ferro naming the group the Wanderers. XS and Gates decide to stay behind and join the original Legion. The "Threeboot" Legion are revealed to be from a re-created Earth-Prime. Kid Flash and XS use Cosmic Treadmills to return the two Legions back to where they came from. Superman returns to the 21st century with Superboy and Kid Flash.

Meanwhile, a powerless Superboy-Prime wakes up on the reborn Earth-Prime. He is reunited with his parents and his girlfriend Lori, who are all horrified by what he's become because they've read copies of the issues published by DC Comics from "Infinite Crisis" to "Legion of 3 Worlds". Superboy-Prime plots his return from his fearful parents' basement, remarking "They'll never get rid of me. I'll always survive."

Earlier team-up

There was a separate adventure known as "The Legion of Three Worlds" prior to Final Crisis. This is one of the Legion's most historical adventures, but it remains undocumented. Superman explains that this is because none of them could remember the exact circumstances of the event due to complications with time travel.[4] Superman later elaborated to Batman that they met two other Legions, and Brainiac 5 theorized they were from parallel Earths.[5]Mon-El says that he barely remembers the event.[1] White Witch says that it revolved around the Tornado Twins.[2]

Brainiac 5 eventually explains these events, as he is the only one to remember them. Professor Zoom targeted the Tornado Twins, and they sought refuge on a parallel world. Zoom sabotaged their Cosmic Treadmill, and the explosion tore apart the Multiverse. This united the three Legions, and they battled Professor Zoom's speed soldiers in the 25th Century. The three Brainiacs redesigned Starman's suit as a map to the Multiverse, and used his gravity powers to send everyone home through black holes. The Legions each went back to their own universe, except the Tornado Twins and their families who remained hidden on Earth-247.[3]